.TH g_vanhove 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_vanhove - calculates Van Hove displacement functions

.B VERSION 4.5
.SH SYNOPSIS
\f3g_vanhove\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-om" " vanhove.xpm "
.BI "\-or" " vanhove_r.xvg "
.BI "\-ot" " vanhove_t.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-sqrt" " real "
.BI "\-fm" " int "
.BI "\-rmax" " real "
.BI "\-rbin" " real "
.BI "\-mmax" " real "
.BI "\-nlevels" " int "
.BI "\-nr" " int "
.BI "\-fr" " int "
.BI "\-rt" " real "
.BI "\-ft" " int "
.SH DESCRIPTION
\&g_vanhove computes the Van Hove correlation function.
\&The Van Hove G(r,t) is the probability that a particle that is at r0
\&at time zero can be found at position r0+r at time t.
\&g_vanhove determines G not for a vector r, but for the length of r.
\&Thus it gives the probability that a particle moves a distance of r
\&in time t.
\&Jumps across the periodic boundaries are removed.
\&Corrections are made for scaling due to isotropic
\&or anisotropic pressure coupling.
\&


\&With option \fB \-om\fR the whole matrix can be written as a function
\&of t and r or as a function of sqrt(t) and r (option \fB \-sqrt\fR).
\&


\&With option \fB \-or\fR the Van Hove function is plotted for one
\&or more values of t. Option \fB \-nr\fR sets the number of times,
\&option \fB \-fr\fR the number spacing between the times.
\&The binwidth is set with option \fB \-rbin\fR. The number of bins
\&is determined automatically.
\&


\&With option \fB \-ot\fR the integral up to a certain distance
\&(option \fB \-rt\fR) is plotted as a function of time.
\&


\&For all frames that are read the coordinates of the selected particles
\&are stored in memory. Therefore the program may use a lot of memory.
\&For options \fB \-om\fR and \fB \-ot\fR the program may be slow.
\&This is because the calculation scales as the number of frames times
\&\fB \-fm\fR or \fB \-ft\fR.
\&Note that with the \fB \-dt\fR option the memory usage and calculation
\&time can be reduced.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-om" " vanhove.xpm" 
.B Output, Opt.
 X PixMap compatible matrix file 

.BI "\-or" " vanhove_r.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-ot" " vanhove_t.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-sqrt"  " real" " 0     " 
 Use sqrt(t) on the matrix axis which binspacing  in sqrt(ps)

.BI "\-fm"  " int" " 0" 
 Number of frames in the matrix, 0 is plot all

.BI "\-rmax"  " real" " 2     " 
 Maximum r in the matrix (nm)

.BI "\-rbin"  " real" " 0.01  " 
 Binwidth in the matrix and for \-or (nm)

.BI "\-mmax"  " real" " 0     " 
 Maximum density in the matrix, 0 is calculate (1/nm)

.BI "\-nlevels"  " int" " 81" 
 Number of levels in the matrix

.BI "\-nr"  " int" " 1" 
 Number of curves for the \-or output

.BI "\-fr"  " int" " 0" 
 Frame spacing for the \-or output

.BI "\-rt"  " real" " 0     " 
 Integration limit for the \-ot output (nm)

.BI "\-ft"  " int" " 0" 
 Number of frames in the \-ot output, 0 is plot all

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
